Exploration of effective potential landscapes using coarse reverse integration.

We describe a reverse integration approach for the exploration of low-dimensional effective potential landscapes. Coarse reverse integration initialized on a ring of coarse states enables efficient navigation on the landscape terrain: Escape from local effective potential wells, detection of saddle points, and identification of significant transition paths between wells. We consider several distinct ring evolution modes: Backward stepping in time, solution arc length, and effective potential. The performance of these approaches is illustrated for a deterministic problem where the energy landscape is known explicitly. Reverse ring integration is then applied to noisy problems where the ring integration routine serves as an outer wrapper around a forward-in-time inner simulator. Two versions of such inner simulators are considered: A Gillespie-type stochastic simulator and a molecular dynamics simulator. In these "equation-free" computational illustrations, estimation techniques are applied to the results of short bursts of inner simulation to obtain the unavailable (in closed-form) quantities (local drift and diffusion coefficient estimates) required for reverse ring integration; this naturally leads to approximations of the effective landscape.

[1]  D. Poppinger,et al.  On the calculation of transition states , 1975 .

[2]  A. Laio,et al.  Escaping free-energy minima , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[3]  Michael E. Henderson,et al.  Multiple Parameter Continuation: Computing Implicitly Defined k-Manifolds , 2002, Int. J. Bifurc. Chaos.

[4]  Michael E. Henderson,et al.  Computing Invariant Manifolds by Integrating Fat Trajectories , 2005, SIAM J. Appl. Dyn. Syst..

[5]  Gerhard Hummer,et al.  Water pulls the strings in hydrophobic polymer collapse , 2007, Proceedings of the National Academy of Sciences.

[6]  Lydia E Kavraki,et al.  Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction , 2006, Proc. Natl. Acad. Sci. USA.

[7]  A. Lucia,et al.  Global terrain methods , 2002 .

[8]  Hitoshi Gotō A frontier mode-following method for mapping saddle points of conformational interconversion in flexible molecules starting from the energy minimum , 1998 .

[9]  Giovanni Ciccotti,et al.  Book Review: Classical and Quantum Dynamics in Condensed Phase Simulations , 1998 .

[10]  G. Hummer,et al.  Reaction coordinates and rates from transition paths. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[11]  F. A. Neugebauer,et al.  Electrochemical oxidation and structural changes of 5,6-dihydrobenzo[c]cinnolines , 1996 .

[12]  García,et al.  Large-amplitude nonlinear motions in proteins. , 1992, Physical review letters.

[13]  Charles L. Brooks,et al.  Simulations of peptide conformational dynamics and thermodynamics , 1993 .

[14]  A. Chakraborty,et al.  A growing string method for determining transition states: comparison to the nudged elastic band and string methods. , 2004, The Journal of chemical physics.

[15]  Yacine Ait-Sahalia Closed-Form Likelihood Expansions for Multivariate Diffusions , 2002, 0804.0758.

[16]  R. Zwanzig Nonequilibrium statistical mechanics , 2001, Physics Subject Headings (PhySH).

[17]  D. Gillespie Exact Stochastic Simulation of Coupled Chemical Reactions , 1977 .

[18]  Ann B. Lee,et al.  Geometric diffusions as a tool for harmonic analysis and structure definition of data: diffusion maps. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[19]  M. Tuckerman,et al.  IN CLASSICAL AND QUANTUM DYNAMICS IN CONDENSED PHASE SIMULATIONS , 1998 .

[20]  H. Jónsson,et al.  Nudged elastic band method for finding minimum energy paths of transitions , 1998 .

[21]  D. A. Mcquarrie Stochastic approach to chemical kinetics , 1967, Journal of Applied Probability.

[22]  Andrew E. Torda,et al.  Local elevation: A method for improving the searching properties of molecular dynamics simulation , 1994, J. Comput. Aided Mol. Des..

[23]  D. Landau,et al.  Efficient, multiple-range random walk algorithm to calculate the density of states. , 2000, Physical review letters.

[24]  G. Henkelman,et al.  A climbing image nudged elastic band method for finding saddle points and minimum energy paths , 2000 .

[25]  A. Pohorille,et al.  Conformational equilibria of terminally blocked single amino acids at the water-hexane interface. A molecular dynamics study. , 1998, The journal of physical chemistry. B.

[26]  Gradisek,et al.  Analysis of time series from stochastic processes , 2000, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[27]  C L Brooks,et al.  Taking a Walk on a Landscape , 2001, Science.

[28]  D. Wales,et al.  A doubly nudged elastic band method for finding transition states. , 2004, The Journal of chemical physics.

[29]  C. W. Gear,et al.  'Coarse' integration/bifurcation analysis via microscopic simulators: Micro-Galerkin methods , 2002 .

[30]  Weiqing Ren,et al.  Higher Order String Method for Finding Minimum Energy Paths , 2003 .

[31]  Dana Schlomiuk,et al.  Bifurcations and Periodic Orbits of Vector Fields , 1993 .

[32]  Ron Elber,et al.  A method for determining reaction paths in large molecules: application to myoglobin , 1987 .

[33]  H. Bernhard Schlegel,et al.  Improved algorithms for reaction path following: Higher‐order implicit algorithms , 1991 .

[34]  D. Gillespie Approximate accelerated stochastic simulation of chemically reacting systems , 2001 .

[35]  A. Voter,et al.  Extending the Time Scale in Atomistic Simulation of Materials Annual Re-views in Materials Research , 2002 .

[36]  Muruhan Rathinam,et al.  The numerical stability of leaping methods for stochastic simulation of chemically reacting systems. , 2004, The Journal of chemical physics.

[37]  W. Miller,et al.  ON FINDING TRANSITION STATES , 1981 .

[38]  R. Miron,et al.  The Step and Slide method for finding saddle points on multidimensional potential surfaces , 2001 .

[39]  Milan Kubíček,et al.  Book-Review - Computational Methods in Bifurcation Theory and Dissipative Structures , 1983 .

[40]  E. Carter,et al.  Ridge method for finding saddle points on potential energy surfaces , 1993 .

[41]  Yacine Aït-Sahalia Maximum Likelihood Estimation of Discretely Sampled Diffusions: A Closed‐form Approximation Approach , 2002 .

[42]  G. Pflug Kernel Smoothing. Monographs on Statistics and Applied Probability - M. P. Wand; M. C. Jones. , 1996 .

[43]  G. G. Stokes "J." , 1890, The New Yale Book of Quotations.

[44]  Bernd Krauskopf,et al.  Modeling and Computations in Dynamical Systems , 2006 .

[45]  H. Risken The Fokker-Planck equation : methods of solution and applications , 1985 .

[46]  Kent R. Wilson,et al.  Shadowing, rare events, and rubber bands. A variational Verlet algorithm for molecular dynamics , 1992 .

[47]  Eric F Darve,et al.  Calculating free energies using average force , 2001 .

[48]  J. Onuchic,et al.  Navigating the folding routes , 1995, Science.

[49]  Ioannis G. Kevrekidis,et al.  Computing in the past with forward integration , 2004 .

[50]  W. E,et al.  Finite temperature string method for the study of rare events. , 2002, Journal of Physical Chemistry B.

[51]  Martin Karplus,et al.  SOLVATION. A MOLECULAR DYNAMICS STUDY OF A DIPEPTIDE IN WATER. , 1979 .

[52]  Mark E. Johnson,et al.  Two-dimensional invariant manifolds and global bifurcations: some approximation and visualization studies , 1997, Numerical Algorithms.

[53]  Elaborating transition interface sampling methods , 2005, cond-mat/0405116.

[54]  Ioannis G. Kevrekidis,et al.  Equation-free: The computer-aided analysis of complex multiscale systems , 2004 .

[55]  J. Simons,et al.  Imposition of geometrical constraints on potential energy surface walking procedures , 1985 .

[56]  G. Henkelman,et al.  A dimer method for finding saddle points on high dimensional potential surfaces using only first derivatives , 1999 .

[57]  Ioannis G. Kevrekidis,et al.  Coarse projective kMC integration: forward/reverse initial and boundary value problems , 2003, nlin/0307016.

[58]  K. Müller,et al.  Location of saddle points and minimum energy paths by a constrained simplex optimization procedure , 1979 .

[59]  J. Baker An algorithm for the location of transition states , 1986 .

[60]  N. Draper,et al.  Applied Regression Analysis , 1966 .

[61]  H. Risken Fokker-Planck Equation , 1996 .

[62]  Christian A. Yates,et al.  Inherent noise can facilitate coherence in collective swarm motion , 2009, Proceedings of the National Academy of Sciences.

[63]  Karl K. Irikura,et al.  Predicting Unexpected Chemical Reactions by Isopotential Searching , 2000 .

[64]  C. Dellago,et al.  Transition path sampling and the calculation of rate constants , 1998 .

[65]  Angelo Lucia,et al.  A Geometric Terrain Methodology for Global Optimization , 2004, J. Glob. Optim..

[66]  Andrew G. Glen,et al.  APPL , 2001 .

[67]  E. Vanden-Eijnden,et al.  String method for the study of rare events , 2002, cond-mat/0205527.

[68]  Gerhard Hummer,et al.  Position-dependent diffusion coefficients and free energies from Bayesian analysis of equilibrium and replica molecular dynamics simulations , 2005 .

[69]  I. Kevrekidis,et al.  Coarse molecular dynamics of a peptide fragment: Free energy, kinetics, and long-time dynamics computations , 2002, physics/0212108.

[70]  Matthew P. Wand,et al.  Kernel Smoothing , 1995 .

[71]  Christophe Chipot,et al.  Exploring the free-energy landscape of a short peptide using an average force. , 2005, The Journal of chemical physics.

[72]  Michael Page,et al.  On evaluating the reaction path Hamiltonian , 1988 .

[73]  B. Nadler,et al.  Diffusion maps, spectral clustering and reaction coordinates of dynamical systems , 2005, math/0503445.